Rebuilding my 7 year old website using a completely new program (Notepad++)

I need to keep the old page URL's exactly the same because they rank really well. I don't want to gamble with redirects.

Using Twitter Bootstrap to do a responsive design. Works great on my PC but when I upload a sample page to the actual site it can't find all the CSS and Image and JS directories it needs.

I can see that it's because the standard Twitter Bootstrap directories for things like the CSS are at different levels from where they got uploaded to the website.

So my question is: How to create paths using things like Relative URL's and maybe a Base URL so that what I am designing on the PC also works on the web when I upload it?